Modeling the Pandemic

Overview

Directories

Directory	Description
.config	Configuration files
build	Main working directory for analysis and modeling
data	Raw data files and data processing scripts
dep	Dependence files for all projects
doc	Data dictionaries and reference tables
res	Static files (i.e., figures)
test	Ongoing testing projects

Usage

1. Install GitHub Desktop from https://docs.github.com/en/desktop/installing-and-authenticating-to-github-desktop/installing-github-desktop
2. Clone this project to the user's desktop from https://github.com/cliandouble08/modeling-the-pandemic.git
   • The cloned project can be updated by pulling updates from GitHub repository using GitHub Desktop.
3. Open the cloned project from the cloning directory.
4. Open "./modeling-the-pandemic.Rproj" before running files in the directory to avoid errors in readr functions.
   • R package installation/loading script is embedded in "./build" files, please run the line source("./dep/file-directory") specific to each file to avoid unnecessary package installation and loading.
   • R packages that are consistently loaded for all files are: readr, tidyr, dplyr, ggplot2
5. Open and run "./build/main.R" to load necessary data files and R packages.
   • Alternative: load "./.RData" to access all history objects and packages.

Notes for specific files

• "./build/main.R" is the primary R file for data analysis post-data-cleaning. Please only visit this file if you do not intend to view anything other than the actual analysis.
• "./dep/package-prep.R" is a generic R template for package installation/loading. You may use it by:
  1. Download the R script to your directory.
  2. Edit the package list required_packages to include your desired packages.
  3. Load the packages by running/embedding source(package-prep-script-directory) in your code.
  4. The script will automatically load the latest version for all listed R packages by default. If a package has not been installed, the script will detect and install the missing package automatically.

Roadmap

1. Data Collection

The project used the following data files from corresponding sources:

Data type	Data	Source	Link
COVID-19	Cases and Deaths	New York Times	https://github.com/nytimes/covid-19-data.git
COVID-19	Hospital capacity
Policy	Policy mapping	Katz, R., Toole, K., Robertson, H. et al. Open data for COVID-19 policy analysis and mapping. Sci Data 10, 491 (2023).	https://doi.org/10.1038/s41597-023-02398-3
Demographic	Demographic and housing estimates	American Community Survey (ACS), U.S. Census Bureau	https://data.census.gov/
Demographic	Education attainments	American Community Survey (ACS), U.S. Census Bureau	https://data.census.gov/
Demographic	Housing Price Index (HPI)	Federal Housing Finance Agency	https://www.fhfa.gov/DataTools/Downloads/Pages/House-Price-Index-Datasets.aspx

2. Data Processing

3. Preliminary Analysis

4. Modeling/Analysis

Additional Toolkits

Configure Git Large File Storage (LFS)

Large data files were uploaded through LFS.

Visit https://docs.github.com/en/repositories/working-with-files/managing-large-files for further instructions.

Contact

Cameron Lian - liancame@grinnell.edu

Instructor: Prof. Shonda Kuiper - kuipers@grinnell.edu

Project Link: https://github.com/cliandouble08/modeling-the-pandemic.git